[REVIEW]: EchemFEM: A Firedrake-based Python package for electrochemical transport

[editorialbot]

Submitting author: @tlroy (Thomas Roy)
Repository: https://github.com/LLNL/echemfem
Branch with paper.md (empty if default branch): joss
Version: v0.0.1
Editor: @RMeli
Reviewers: @sudarshanv01, @alizma, @TomTranter
Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/24fc67bb5ebbf43af1db08488741cb06/status.svg)](https://joss.theoj.org/papers/24fc67bb5ebbf43af1db08488741cb06)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@sudarshanv01 & @alizma & @TomTranter, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @RMeli know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @sudarshanv01

📝 Checklist for @alizma

📝 Checklist for @TomTranter

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1029.3 files/s, 152300.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          43           1245            645           6828
GLSL                             7             74             35            445
reStructuredText                 9            173             86            297
Markdown                         5             54              0            205
TeX                              1             15              0            160
Perl                             2             24             18            100
YAML                             1              0              0             43
DOS Batch                        1              8              1             26
make                             2              5              7             12
-------------------------------------------------------------------------------
SUM:                            71           1598            792           8116
-------------------------------------------------------------------------------

Commit count by author:

    97	Thomas Roy
     6	Jack Guo
     4	ehlinger
     2	Nitish Govindarajan
     2	Tiras Lin
     2	Victoria Ehlinger

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1495

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jcp.2022.111859 is OK
- 10.1103/PRXEnergy.2.033010 is OK
- 10.25561/104839 is OK
- 10.2172/1968587 is OK
- 10.1007/s10562-015-1495-6 is OK
- 10.1021/jp402181e is OK
- 10.1149/2754-2734/acff0b is OK
- 10.1137/17M1133208 is OK
- 10.21105/joss.01292 is OK
- 10.1007/s00158-022-03249-2 is OK
- 10.1016/j.carbon.2023.01.044 is OK

MISSING DOIs

- No DOI given, and none found for title: OpenFOAM
- No DOI given, and none found for title: Gmsh: A 3-D finite element mesh generator with bui...
- No DOI given, and none found for title: PETSc Web page
- 10.1149/osf.io/67ckj may be a valid DOI for title: Python battery mathematical modelling (PyBaMM)

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[tlroy]

@editorialbot commands

[editorialbot]

Hello @tlroy, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[tlroy]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/nme.2579 is OK
- 10.1016/j.jcp.2022.111859 is OK
- 10.1103/PRXEnergy.2.033010 is OK
- 10.25561/104839 is OK
- 10.2172/1968587 is OK
- 10.1007/s10562-015-1495-6 is OK
- 10.1021/jp402181e is OK
- 10.1149/2754-2734/acff0b is OK
- 10.5334/jors.309 is OK
- 10.1137/17M1133208 is OK
- 10.21105/joss.01292 is OK
- 10.1007/s00158-022-03249-2 is OK
- 10.1016/j.carbon.2023.01.044 is OK

MISSING DOIs

- No DOI given, and none found for title: OpenFOAM
- No DOI given, and none found for title: PETSc Web page

INVALID DOIs

- None

[sudarshanv01]

Review checklist for @sudarshanv01

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/LLNL/echemfem?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tlroy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[alizma]

Review checklist for @alizma

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/LLNL/echemfem?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tlroy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[TomTranter]

Review checklist for @TomTranter

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/LLNL/echemfem?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tlroy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[RMeli]

Hello everyone! I see that the checklist are being filled, and issues are being opened in the repository. Thanks for all the work, do let me know if you have questions or need help.

[tlroy]

@TomTranter @sudarshanv01 @alizma. I think I answered all the issues that were opened. Please let me know if there is anything else to be done.

[TomTranter]

All good for me

[sudarshanv01]

Also fine for me!

[RMeli]

Thank you @TomTranter and @sudarshanv01 for completing the review.

@alizma how is your review coming along? Please let me know if you need any support.

[alizma]

Sorry for the delay, I've been a bit tied up with the end of this academic year. I hope to finish my review by the end of the week.

[alizma]

I think the package satisfies all the technical requirements, but I'm a bit concerned with some of the examples failing and a lack of documentation for some of the solvers. @tlroy is there any chance you could take a look?

[RMeli]

No worries @alizma.

but I'm a bit concerned with some of the examples failing and a lack of documentation for some of the solvers

I see you have LLNL/echemfem#14 opened for the documentation. Would you mind opening issues for the examples failing, so that the authors/developers have actionable issues to work on? Thanks.

[alizma]

Yes, I added the errors I ran into with examples to an existing issue about errors in the examples: LLNL/echemfem#10, which has some discussion about fixes.

[RMeli]

Thanks for pointing it out, I missed these additional comments on LLNL/echemfem#10.